Intracellular amastigotes of the protozoan parasite Leishmania mexicana secrete a macromolecular proteophosphoglycan (aPPG) into the phagolysosome of their host cell, the mammalian macrophage. The structures of aPPG glycans were analyzed by a combination of high pH anion exchange high pressure liquid chromatography, gas chromatography-mass spectrometry, enzymatic digestions, electrospray-mass spectrometry as well as 1H and 31P NMR spectroscopy. Some glycans are identical to oligosaccharides known from Leishmania mexicana promastigote lipophosphoglycan and secreted acid phosphatase. However, the majority of the aPPG glycans represent amastigote stage-specific and novel structures. These include neutral glycans ([Glcbeta1-3]1-2Galbeta1-4Man, Galbeta1-3Galbeta1-4Man, Galbeta1-3Glcbeta1-3Galbeta1-4Man), several monophosphorylated glycans containing the conserved phosphodisaccharide backbone (R-3-[PO4-6-Gal]beta1-4Man) but carrying stage-specific modifications (R = Galbeta1-, [Glcbeta1-3]1-2Glcbeta1-), and monophosphorylated aPPG tri- and tetrasaccharides that are uniquely phosphorylated on the terminal hexose (PO4-6-Glcbeta1-3Galbeta1-4Man, PO4-6-Glcbeta1-3Glcbeta1-3Galbeta1-4Man, PO4-6-Galbeta1-3Glcbeta1-3Galbeta1-4Man). In addition aPPG contains highly unusual di- and triphosphorylated glycans whose major species are PO4-6-Glcbeta1-3Glcbeta1-3[PO4-6-Gal]beta1-4Man, PO4-6-Galbeta1-3Glcbeta1-3[PO4-6-Gal]beta1-4Man, PO4-6-Galbeta1-3Glcbeta1-3Glcbeta1-3[PO4-6-Gal]beta1-+ ++4Man, PO4-6-Glcbeta1-3[PO4-6-Glc]beta1-3[PO4-6-Gal]beta1-4Man, PO4-6-Galbeta1-3[PO4-6-Glc]beta1-3Glcbeta1-3[PO4-6-Gal]beta1 -4Man, and PO4-6-Glcbeta1-3[PO4-6-Glc]beta1-3Glcbeta1-3[PO4-6-Gal]beta1 -4Man. These glycans are linked together by the conserved phosphodiester R-Manalpha1-PO4-6-Gal-R or the novel phosphodiester R-Manalpha1-PO4-6-Glc-R and are connected to Ser(P) of the protein backbone most likely via the linkage R-Manalpha1-PO4-Ser. The variety of stage-specific glycan structures in Leishmania mexicana aPPG suggests the presence of developmentally regulated amastigote glycosyltransferases which may be potential anti-parasite drug targets.